The structural transformations of graphene defects have been extensively researched through aberration-corrected transmission electron microscopy (AC-TEM) and theoretical calculations. For a long time, a core concept in understanding the structural evolution of graphene defects has been the Stone-Thrower-Wales (STW)-type bond rotation. In this study, we show that undercoordinated atoms induce bond formation and breaking, with much lower energy barriers than the STW-type bond rotation. We refer to them as mediator atoms due to their mediating role in the breaking and forming of bonds. Here, we report the direct observation of mediator atoms in graphene defect structures using AC-TEM and annular dark-field scanning TEM (ADF-STEM) and explain their catalytic role by tight-binding molecular dynamics (TBMD) simulations and image simulations based on density functional theory (DFT) calculations. The study of mediator atoms will pave a new way for understanding not only defect transformation but also the growth mechanisms in two-dimensional materials.